Serialized Form


Package org.jmol.adapter.smarter

Class org.jmol.adapter.smarter.Atom extends javax.vecmath.Point3f implements Serializable

Serialized Fields

atomSetIndex

int atomSetIndex

atomIndex

int atomIndex

bsSymmetry

java.util.BitSet bsSymmetry

atomSite

int atomSite

elementSymbol

java.lang.String elementSymbol

elementNumber

short elementNumber

atomName

java.lang.String atomName

formalCharge

int formalCharge

partialCharge

float partialCharge

vectorX

float vectorX

vectorY

float vectorY

vectorZ

float vectorZ

bfactor

float bfactor

occupancy

int occupancy

radius

float radius

isHetero

boolean isHetero

atomSerial

int atomSerial

chainID

char chainID

alternateLocationID

char alternateLocationID

group3

java.lang.String group3

sequenceNumber

int sequenceNumber

insertionCode

char insertionCode

anisoBorU

float[] anisoBorU

ellipsoid

java.lang.Object[] ellipsoid

Package org.jmol.appletwrapper

Class org.jmol.appletwrapper.AppletWrapper extends java.applet.Applet implements Serializable

Serialized Fields

wrappedAppletClassName

java.lang.String wrappedAppletClassName

preloadImageName

java.lang.String preloadImageName

preloadTextMessage

java.lang.String preloadTextMessage

preloadThreadCount

int preloadThreadCount

preloadClassNames

java.lang.String[] preloadClassNames

preloadClassIndex

int preloadClassIndex

previousClassName

java.lang.String previousClassName

needToCompleteInitialization

boolean needToCompleteInitialization

preloadImageReadyForDisplay

boolean preloadImageReadyForDisplay

preloadImagePainted

boolean preloadImagePainted

preloadImage

java.awt.Image preloadImage

mediaTracker

java.awt.MediaTracker mediaTracker

bgcolor

java.awt.Color bgcolor

textColor

java.awt.Color textColor

wrappedApplet

WrappedApplet wrappedApplet

startTime

long startTime

clockX

int clockX

clockBaseline

int clockBaseline

clockWidth

int clockWidth

fontSize

int fontSize

font

java.awt.Font font

fontMetrics

java.awt.FontMetrics fontMetrics

fontAscent

int fontAscent

fontHeight

int fontHeight

isSigned

boolean isSigned

Package org.jmol.export.dialog

Class org.jmol.export.dialog.Dialog extends javax.swing.JPanel implements Serializable

Serialized Fields

extensions

java.lang.String[] extensions

choice

java.lang.String choice

extension

java.lang.String extension

qSliderJPEG

javax.swing.JSlider qSliderJPEG

qSliderPNG

javax.swing.JSlider qSliderPNG

cb

javax.swing.JComboBox cb

qPanelJPEG

javax.swing.JPanel qPanelJPEG

qPanelPNG

javax.swing.JPanel qPanelPNG

openPreview

FilePreview openPreview

initialFile

java.io.File initialFile

Class org.jmol.export.dialog.FileChooser extends javax.swing.JFileChooser implements Serializable

Serialized Fields

dialogLocation

java.awt.Point dialogLocation

dialogSize

java.awt.Dimension dialogSize

dialog

javax.swing.JDialog dialog

Class org.jmol.export.dialog.FilePreview extends javax.swing.JPanel implements Serializable

Serialized Fields

active

javax.swing.JCheckBox active

append

javax.swing.JCheckBox append

chooser

javax.swing.JFileChooser chooser

display

FilePreview.JmolPanel display

Package org.jmol.jcamp

Class org.jmol.jcamp.SaisieDlg extends java.awt.Dialog implements Serializable

Serialized Fields

Ok

java.awt.Button Ok

Annuler

java.awt.Button Annuler

Saisie

java.awt.TextField Saisie

OkStatus

boolean OkStatus

fin

boolean fin

Class org.jmol.jcamp.Visua extends java.applet.Applet implements Serializable

Serialized Fields

My_ZoneVisu

ZoneVisu My_ZoneVisu

My_Thread

java.lang.Thread My_Thread

_graphDataUtils

GraphCharacteristics _graphDataUtils

texte

java.util.Vector<E> texte

nbLignes

int nbLignes

shitty_starting_constant

int shitty_starting_constant

Firstx

double Firstx

Lastx

double Lastx

YFactor

double YFactor

Nbpoints

int Nbpoints

nmr_observe_frequency

double nmr_observe_frequency

TexteTitre

java.lang.String TexteTitre

x_units

java.lang.String x_units

y_units

java.lang.String y_units

Datatype

java.lang.String Datatype

Load_File

java.awt.Button Load_File

Zoom_In

java.awt.Button Zoom_In

Zoom_Back

java.awt.Button Zoom_Back

Zoom_Out

java.awt.Button Zoom_Out

Reverse

java.awt.Checkbox Reverse

Grid

java.awt.Checkbox Grid

Integrate

java.awt.Checkbox Integrate

Find_Peak

java.awt.Button Find_Peak

JCamp

java.awt.Button JCamp

Fenetre_Load_File

java.awt.Frame Fenetre_Load_File

Dialogue_Load_File

SaisieDlg Dialogue_Load_File

contexte

java.applet.AppletContext contexte

clickable_peaks_frame_name

java.lang.String clickable_peaks_frame_name

Flag_Zoomin

boolean Flag_Zoomin

Flag_Zoomback

boolean Flag_Zoomback

Flag_Zoomout

boolean Flag_Zoomout

Flag_Reverse

boolean Flag_Reverse

Flag_Integrate

boolean Flag_Integrate

Flag_Dialogue_File_Enabled

boolean Flag_Dialogue_File_Enabled

Flag_Redraw

boolean Flag_Redraw

Flag_Find_Peak

boolean Flag_Find_Peak

Flag_Write_JCamp

boolean Flag_Write_JCamp

isActive

boolean isActive

hasPrivilege

boolean hasPrivilege

inNavigator

boolean inNavigator

inExplorer

boolean inExplorer

openDialog

java.awt.FileDialog openDialog

saveDialog

java.awt.FileDialog saveDialog

Current_Error

java.lang.String Current_Error

Class org.jmol.jcamp.ZoneVisu extends java.awt.Canvas implements Serializable

Serialized Fields

_graphDataUtils

GraphCharacteristics _graphDataUtils

Firstx

double Firstx

Lastx

double Lastx

Miny

double Miny

Maxy

double Maxy

YFactor

double YFactor

xLowerLimit

int xLowerLimit

xUpperLimit

int xUpperLimit

nbLignes

int nbLignes

Nbpoints

int Nbpoints

TexteTitre

java.lang.String TexteTitre

x_units

java.lang.String x_units

y_units

java.lang.String y_units

typedata

int typedata

reverse

boolean reverse

RealFirstx

double RealFirstx

RealLastx

double RealLastx

Last_RealFirstx

double Last_RealFirstx

Last_RealLastx

double Last_RealLastx

Last_Firstx

double Last_Firstx

Last_Lastx

double Last_Lastx

Sav_Firstx

double Sav_Firstx

Sav_Lastx

double Sav_Lastx

Flag_Clickable_Peaks

boolean Flag_Clickable_Peaks

Nb_Clickable_Peaks

int Nb_Clickable_Peaks

Peak_Start

double[] Peak_Start

Peak_Stop

double[] Peak_Stop

Peak_Html

java.lang.String[] Peak_Html

Flag_Load_Now_Html

boolean Flag_Load_Now_Html

Name_Load_Now_Html

java.lang.String Name_Load_Now_Html

Sav_Nbpoints_a_tracer

int Sav_Nbpoints_a_tracer

Nbpoints_a_tracer

int Nbpoints_a_tracer

prempoint

int prempoint

Y_Values

java.lang.String Y_Values

ShowTitle

java.lang.String ShowTitle

shitty_starting_constant

int shitty_starting_constant

tableau_points

double[] tableau_points

tableau_integrate

double[] tableau_integrate

Incrx

double Incrx

Multx

double Multx

Multy

double Multy

Maxintegrate

double Maxintegrate

x

double x

y

double y

ax

double ax

ay

double ay

xd

double xd

xf

double xf

largeur

int largeur

hauteur

int hauteur

largeur_gfx

int largeur_gfx

hauteur_gfx

int hauteur_gfx

decalx_gfx

int decalx_gfx

decaly_gfx

int decaly_gfx

hauteur_bandeau

int hauteur_bandeau

Flag_Grid

boolean Flag_Grid

Flag_Reverse

boolean Flag_Reverse

Flag_Integrate

boolean Flag_Integrate

location_textetitre

int location_textetitre

BufImg

java.awt.Image BufImg

BufGra

java.awt.Graphics BufGra

SavBufImg

java.awt.Image SavBufImg

SavBufGra

java.awt.Graphics SavBufGra

ZoomBufImg

java.awt.Image ZoomBufImg

ZoomBufGra

java.awt.Graphics ZoomBufGra

x1_zoom

int x1_zoom

x2_zoom

int x2_zoom

indice

int indice

Un_Nombre

java.lang.String Un_Nombre

Package org.jmol.modelset

Class org.jmol.modelset.Atom extends Point3fi implements Serializable

Serialized Fields

group

Group group

atomIndex

int atomIndex

atomSymmetry

java.util.BitSet atomSymmetry

atomSite

int atomSite

userDefinedVanDerWaalRadius

float userDefinedVanDerWaalRadius

modelIndex

short modelIndex

atomicAndIsotopeNumber

short atomicAndIsotopeNumber

formalChargeAndFlags

byte formalChargeAndFlags

valence

byte valence

alternateLocationID

char alternateLocationID

madAtom

short madAtom

colixAtom

short colixAtom

paletteID

byte paletteID

bonds

Bond[] bonds

nBondsDisplayed

int nBondsDisplayed

nBackbonesDisplayed

int nBackbonesDisplayed

clickabilityFlags

int clickabilityFlags

shapeVisibilityFlags

int shapeVisibilityFlags

isSimple

boolean isSimple

Class org.jmol.modelset.Bond.BondSet extends java.util.BitSet implements Serializable

Serialized Fields

associatedAtoms

int[] associatedAtoms

Package org.jmol.smiles

Class org.jmol.smiles.InvalidSmilesException extends java.lang.Exception implements Serializable


Package org.jmol.util

Class org.jmol.util.JpegEncoder extends java.awt.Frame implements Serializable

Serialized Fields

outStream

java.io.BufferedOutputStream outStream

JpegObj

JpegInfo JpegObj

Huf

Huffman Huf

dct

DCT dct

Quality

int Quality

Class org.jmol.util.Point3fi extends javax.vecmath.Point3f implements Serializable

Serialized Fields

screenX

int screenX

screenY

int screenY

screenZ

int screenZ

screenDiameter

short screenDiameter

Package org.openscience.jmol.app

Class org.openscience.jmol.app.AboutDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

html

javax.swing.JEditorPane html

Class org.openscience.jmol.app.AtomSetChooser extends javax.swing.JFrame implements Serializable

Serialized Fields

animThread

java.lang.Thread animThread

propertiesTextArea

javax.swing.JTextArea propertiesTextArea

tree

javax.swing.JTree tree

treeModel

javax.swing.tree.DefaultTreeModel treeModel

viewer

JmolViewer viewer

repeatCheckBox

javax.swing.JCheckBox repeatCheckBox

selectSlider

javax.swing.JSlider selectSlider

infoLabel

javax.swing.JLabel infoLabel

fpsSlider

javax.swing.JSlider fpsSlider

amplitudeSlider

javax.swing.JSlider amplitudeSlider

periodSlider

javax.swing.JSlider periodSlider

scaleSlider

javax.swing.JSlider scaleSlider

radiusSlider

javax.swing.JSlider radiusSlider

saveChooser

javax.swing.JFileChooser saveChooser

indexes

int[] indexes
Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf.


currentIndex

int currentIndex

Class org.openscience.jmol.app.ConsoleTextArea extends javax.swing.JTextArea implements Serializable

Class org.openscience.jmol.app.DisplayPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

status

StatusBar status

guimap

GuiMap guimap

viewer

JmolViewer viewer

displaySpeed

java.lang.String displaySpeed

startupDimension

java.awt.Dimension startupDimension

haveDisplay

boolean haveDisplay

showPaintTime

boolean showPaintTime

dimSize

java.awt.Dimension dimSize

rectClip

java.awt.Rectangle rectClip

homeAction

DisplayPanel.HomeAction homeAction

defineCenterAction

DisplayPanel.DefineCenterAction defineCenterAction

frontAction

javax.swing.Action frontAction

topAction

javax.swing.Action topAction

bottomAction

javax.swing.Action bottomAction

rightAction

javax.swing.Action rightAction

leftAction

javax.swing.Action leftAction

hydrogensAction

javax.swing.Action hydrogensAction

measurementsAction

javax.swing.Action measurementsAction

perspectiveAction

javax.swing.Action perspectiveAction

axesAction

javax.swing.Action axesAction

boundboxAction

javax.swing.Action boundboxAction

deleteAction

javax.swing.Action deleteAction

zoomAction

javax.swing.Action zoomAction

xlateAction

javax.swing.Action xlateAction

menuListener

javax.swing.event.MenuListener menuListener

timeBegin

long timeBegin

lastMotionEventNumber

int lastMotionEventNumber

Class org.openscience.jmol.app.FileTyper extends javax.swing.JPanel implements Serializable

Serialized Fields

useFileExtensionCheckBox

javax.swing.JCheckBox useFileExtensionCheckBox

fileTypeLabel

javax.swing.JLabel fileTypeLabel

fileTypeComboBox

javax.swing.JComboBox fileTypeComboBox

useFileExtension

boolean useFileExtension

choices

java.lang.String[] choices

defaultTypeIndex

int defaultTypeIndex

fileType

java.lang.String fileType

Class org.openscience.jmol.app.HelpDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

html

javax.swing.JEditorPane html

Class org.openscience.jmol.app.Jmol extends javax.swing.JPanel implements Serializable

Serialized Fields

viewer

JmolViewer viewer
The data model.


display

DisplayPanel display

status

StatusBar status

preferencesDialog

PreferencesDialog preferencesDialog

measurementTable

MeasurementTable measurementTable

recentFiles

RecentFilesDialog recentFiles

scriptWindow

ScriptWindow scriptWindow

atomSetChooser

AtomSetChooser atomSetChooser

executeScriptAction

Jmol.ExecuteScriptAction executeScriptAction

frame

javax.swing.JFrame frame

jmolpopup

JmolPopup jmolpopup

language

java.lang.String language

guimap

GuiMap guimap

startupWidth

int startupWidth

startupHeight

int startupHeight

pcs

java.beans.PropertyChangeSupport pcs

splash

Splash splash

modelAdapter

JmolAdapter modelAdapter

appletContext

java.lang.String appletContext

commands

java.util.Hashtable<K,V> commands

menuItems

java.util.Hashtable<K,V> menuItems

menubar

javax.swing.JMenuBar menubar

toolbar

javax.swing.JToolBar toolbar

exportAction

Jmol.ExportAction exportAction

povrayAction

Jmol.PovrayAction povrayAction

toWebAction

Jmol.ToWebAction toWebAction

writeAction

Jmol.WriteAction writeAction

printAction

Jmol.PrintAction printAction

copyImageAction

Jmol.CopyImageAction copyImageAction

copyScriptAction

Jmol.CopyScriptAction copyScriptAction

pasteClipboardAction

Jmol.PasteClipboardAction pasteClipboardAction

viewMeasurementTableAction

Jmol.ViewMeasurementTableAction viewMeasurementTableAction

qualityJPG

int qualityJPG

qualityPNG

int qualityPNG

imageType

java.lang.String imageType

defaultActions

javax.swing.Action[] defaultActions
Actions defined by the Jmol class


webExport

WebExport webExport

Class org.openscience.jmol.app.MeasurementTable extends javax.swing.JDialog implements Serializable

Serialized Fields

viewer

JmolViewer viewer

measurementTable

javax.swing.JTable measurementTable

measurementTableModel

MeasurementTable.MeasurementTableModel measurementTableModel

selectedMeasurementRow

int selectedMeasurementRow

deleteButton

javax.swing.JButton deleteButton

deleteAllButton

javax.swing.JButton deleteAllButton

stringClass

java.lang.Class<T> stringClass

Class org.openscience.jmol.app.PovrayDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

povrayPathButton

javax.swing.JButton povrayPathButton

goButton

javax.swing.JButton goButton

saveField

javax.swing.JTextField saveField

savePathLabel

javax.swing.JTextField savePathLabel

outputWidth

int outputWidth

outputHeight

int outputHeight

povrayPathLabel

javax.swing.JTextField povrayPathLabel

runPovCheck

javax.swing.JCheckBox runPovCheck

allFramesCheck

javax.swing.JCheckBox allFramesCheck

antiAliasCheck

javax.swing.JCheckBox antiAliasCheck

displayWhileRenderingCheck

javax.swing.JCheckBox displayWhileRenderingCheck

imageSizeWidth

javax.swing.JLabel imageSizeWidth

imageSizeTextWidth

javax.swing.JFormattedTextField imageSizeTextWidth

imageSizeHeight

javax.swing.JLabel imageSizeHeight

imageSizeTextHeight

javax.swing.JFormattedTextField imageSizeTextHeight

imageSizeRatioBox

javax.swing.JCheckBox imageSizeRatioBox

imageSizeRatioCombo

javax.swing.JComboBox imageSizeRatioCombo

outputFormatCheck

javax.swing.JCheckBox outputFormatCheck

outputFormatCombo

javax.swing.JComboBox outputFormatCombo

outputAlphaCheck

javax.swing.JCheckBox outputAlphaCheck

mosaicPreviewCheck

javax.swing.JCheckBox mosaicPreviewCheck

mosaicPreviewStart

javax.swing.JLabel mosaicPreviewStart

mosaicPreviewComboStart

javax.swing.JComboBox mosaicPreviewComboStart

mosaicPreviewEnd

javax.swing.JLabel mosaicPreviewEnd

mosaicPreviewComboEnd

javax.swing.JComboBox mosaicPreviewComboEnd

outputExtension

java.lang.String outputExtension

outputFileType

java.lang.String outputFileType

Class org.openscience.jmol.app.PreferencesDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

autoBond

boolean autoBond

showHydrogens

boolean showHydrogens

showMeasurements

boolean showMeasurements

perspectiveDepth

boolean perspectiveDepth

showAxes

boolean showAxes

showBoundingBox

boolean showBoundingBox

axesOrientationRasmol

boolean axesOrientationRasmol

openFilePreview

boolean openFilePreview

clearConsoleButton

boolean clearConsoleButton

minBondDistance

float minBondDistance

bondTolerance

float bondTolerance

marBond

short marBond

percentVdwAtom

int percentVdwAtom

bButton

javax.swing.JButton bButton

pButton

javax.swing.JButton pButton

tButton

javax.swing.JButton tButton

eButton

javax.swing.JButton eButton

vButton

javax.swing.JButton vButton

abYes

javax.swing.JRadioButton abYes

abNo

javax.swing.JRadioButton abNo

vdwPercentSlider

javax.swing.JSlider vdwPercentSlider

bdSlider

javax.swing.JSlider bdSlider

bwSlider

javax.swing.JSlider bwSlider

btSlider

javax.swing.JSlider btSlider

cH

javax.swing.JCheckBox cH

cM

javax.swing.JCheckBox cM

cbPerspectiveDepth

javax.swing.JCheckBox cbPerspectiveDepth

cbShowAxes

javax.swing.JCheckBox cbShowAxes

cbShowBoundingBox

javax.swing.JCheckBox cbShowBoundingBox

cbAxesOrientationRasmol

javax.swing.JCheckBox cbAxesOrientationRasmol

cbOpenFilePreview

javax.swing.JCheckBox cbOpenFilePreview

cbClearConsoleButton

javax.swing.JCheckBox cbClearConsoleButton

originalSystemProperties

java.util.Properties originalSystemProperties

jmolDefaultProperties

java.util.Properties jmolDefaultProperties

currentProperties

java.util.Properties currentProperties

prefsAction

PreferencesDialog.PrefsAction prefsAction

commands

java.util.Hashtable<K,V> commands

viewer

JmolViewer viewer

guimap

GuiMap guimap

checkBoxListener

java.awt.event.ItemListener checkBoxListener

applyButton

javax.swing.JButton applyButton

jmolDefaultsButton

javax.swing.JButton jmolDefaultsButton

rasmolDefaultsButton

javax.swing.JButton rasmolDefaultsButton

cancelButton

javax.swing.JButton cancelButton

okButton

javax.swing.JButton okButton

Class org.openscience.jmol.app.ScriptWindow extends javax.swing.JDialog implements Serializable

Serialized Fields

console

ConsoleTextPane console

closeButton

javax.swing.JButton closeButton

runButton

javax.swing.JButton runButton

haltButton

javax.swing.JButton haltButton

clearButton

javax.swing.JButton clearButton

historyButton

javax.swing.JButton historyButton

stateButton

javax.swing.JButton stateButton

helpButton

javax.swing.JButton helpButton

undoButton

javax.swing.JButton undoButton

redoButton

javax.swing.JButton redoButton

viewer

JmolViewer viewer

isError

boolean isError

execThread

ScriptWindow.ExecuteCommandThread execThread

undoStack

java.lang.String[] undoStack

undoPointer

int undoPointer

undoSaved

boolean undoSaved

Class org.openscience.jmol.app.Splash extends java.awt.Window implements Serializable

Serialized Fields

splashImage

java.awt.Image splashImage

imgWidth

int imgWidth

imgHeight

int imgHeight

status

java.lang.String status

textY

int textY

statusTop

int statusTop

Class org.openscience.jmol.app.WhatsNewDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

html

javax.swing.JEditorPane html

Package org.openscience.jmol.app.webexport

Class org.openscience.jmol.app.webexport.Orbitals extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

OrbopenButton

javax.swing.JButton OrbopenButton

OrbdeleteButton

javax.swing.JButton OrbdeleteButton

CooropenButton

javax.swing.JButton CooropenButton

saveButton

javax.swing.JButton saveButton

Coorfile

javax.swing.JTextField Coorfile

appletPath

javax.swing.JTextField appletPath

fc

javax.swing.JFileChooser fc

OrbList

javax.swing.JList OrbList

RenderMode

javax.swing.JComboBox RenderMode

FormatBox

javax.swing.JComboBox FormatBox

Class org.openscience.jmol.app.webexport.Test extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

StateButton

javax.swing.JButton StateButton

FileButton

javax.swing.JButton FileButton

PathButton

javax.swing.JButton PathButton

movetoTime

javax.swing.JButton movetoTime

StringtoScriptButton

javax.swing.JButton StringtoScriptButton

appletPath

javax.swing.JTextField appletPath

arrayListHandler

ArrayListTransferHandler arrayListHandler

fc

javax.swing.JFileChooser fc

viewer

Viewer viewer

Class org.openscience.jmol.app.webexport.WebExport extends javax.swing.JPanel implements Serializable

Class org.openscience.jmol.app.webexport.WebMaker extends javax.swing.JPanel implements Serializable